Contacts of the strand formed by residues 4038 - 4043 (chain B) in PDB entry 4O2W
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with CYS4038 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4009B GLN* 3.8 1.6 - - - -
4035B GLY* 2.9 28.4 + - - -
4036B GLN 3.1 16.9 - - - +
4037B ASN* 1.3 80.5 - - - +
4039B THR* 1.3 64.3 + - - +
4040B PHE* 3.8 23.3 - - + -
4051B CYS 3.3 12.3 - - - +
4053B GLU 4.1 4.7 - - - +
4058B ARG* 3.6 25.1 - - - -
4059B LEU* 3.7 18.2 - - + -
4086B THR* 4.4 3.6 - - - -
4354B HIS* 3.2 7.8 - - - -
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Residues in contact with THR4039 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4001B LEU* 5.0 3.6 - - + -
4009B GLN 2.7 27.1 + - - +
4026B PHE* 3.9 15.9 - - + -
4032B VAL* 3.7 29.4 - - + -
4033B ILE 3.5 10.3 - - - +
4034B CYS* 4.4 7.0 - - - -
4038B CYS* 1.3 71.4 - - - +
4040B PHE* 1.3 66.3 + - - +
4050B ALA* 3.3 4.2 - - - +
4051B CYS* 2.9 40.0 + - - +
4070B LEU* 4.4 1.0 - - - +
4354B HIS* 2.9 18.7 + - - -
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Residues in contact with PHE4040 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4032B VAL* 3.4 7.1 - - - +
4033B ILE* 2.8 43.7 + - + +
4038B CYS* 3.8 20.4 - - + -
4039B THR* 1.3 74.8 - - - +
4041B VAL* 1.3 65.5 + - - +
4048B VAL* 4.8 0.2 - - + -
4049B LEU 3.2 8.5 - - - +
4050B ALA* 3.6 27.8 - - + -
4058B ARG* 3.5 23.8 - - + -
4059B LEU* 4.3 5.6 - - + -
4070B LEU* 5.2 0.2 - - - -
4073B ILE* 4.0 11.7 - - + -
4084B LEU* 3.9 36.1 - - + -
4086B THR* 3.6 24.9 - - + -
4094B SER* 3.7 10.5 - - - -
4106B TRP* 3.9 15.7 - + - -
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Residues in contact with VAL4041 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4026B PHE* 3.6 35.2 - - + +
4029B ALA* 3.5 35.4 - - + +
4031B GLN 3.3 5.6 - - - +
4032B VAL* 4.5 1.6 - - + -
4040B PHE* 1.3 80.0 - - - +
4042B ILE* 1.3 70.8 + - - +
4043B GLN* 4.2 4.3 - - + +
4047B THR 3.7 0.3 - - - +
4048B VAL* 3.3 7.8 - - - +
4049B LEU* 2.9 47.6 + - + +
4070B LEU* 3.7 18.4 - - + -
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Residues in contact with ILE4042 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4029B ALA* 3.8 0.3 - - - -
4030B GLN* 2.8 31.2 + - + +
4031B GLN* 3.0 45.6 + - + +
4033B ILE* 4.1 11.9 - - + -
4041B VAL* 1.3 79.8 - - - +
4043B GLN* 1.3 67.8 + - - +
4046B GLY* 4.5 3.4 - - - -
4047B THR 3.5 7.4 - - - +
4048B VAL* 4.6 5.4 - - + -
4081B VAL* 3.4 31.4 - - + +
4083B GLN* 3.9 6.7 - - - +
4084B LEU* 3.8 38.4 - - + +
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Residues in contact with GLN4043 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4028B GLN* 3.7 50.4 + - - +
4030B GLN* 4.0 3.3 - - - +
4041B VAL* 4.6 2.2 - - + -
4042B ILE* 1.3 85.4 - - - +
4044B ALA* 1.3 66.3 + - - +
4045B ASN* 3.3 33.5 + - - +
4046B GLY 3.1 10.7 + - - -
4047B THR* 2.9 19.7 + - - +
4049B LEU* 3.7 32.7 - - + +
4081B VAL 5.0 0.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il